San Carlos, CA-based Atreca and the Seattle non-profit will work together to speed up progress toward the development of new vaccines and drugs. Atreca could also receive project grants under the long-term collaboration, which will use the company’s novel antibody detection platform to support the foundation’s longstanding global fight against infectious diseases.

But the potential of Atreca’s technology platform could reach well beyond its use as a clinical trial support tool, Serafini says. It could also identify new drug targets in a range of diseases by cataloging the antibodies produced in response to infections, tumors, and other conditions that activate the immune system.

“Those antibodies provide a rich trove of potential therapeutics and diagnostics,’’ Serafini says. Atreca’s ultimate aim is to become a developer of new medical treatments.

The company was founded in 2010 to commercialize the discoveries of one of its co-founders, Stanford University professor of medicine William H Robinson. Atreca recently negotiated an exclusive license for the technology from Stanford. Its seed capital came from angel investors, including several Atreca co-founders, and Mission Bay Capital, an independent venture firm managed by leaders of a University of California research consortium, QB3.

Atreca’s method, called “Immune Repertoire Capture,” can take a quick snapshot of the many types of antibodies people are producing at a particular time, says Serafini.

Do this when somebody is fighting a cold bug, say, and you will find that his immune system has put out a cloud of different antibodies, each reacting uniquely to some feature of the microbe, or antigen, that the body has recognized as a foreign enemy.

Searching for patterns amid that antibody population can provide clues for scientists who want to make drugs or vaccines to fight the germ.

“It tells you what the body thought was important,” says Serafini, a Stanford PhD, former UC Berkeley faculty member, and former executive with two biopharmaceutical companies, Nuon Therapeutics and Renovis. A potent antibody itself can become a drug, or scientists can create a vaccine using an antigen that will spur the body to manufacture that antibody.

The startup plans to survey the immune systems of multiple patients to amplify the clues in drug development.

Antibodies from people who get well fast would provide the best leads, Serafini proposes. “Here are five antigens on this bug, and these are the ones targeted by 85 percent of people who have a good outcome.”

What makes Atreca’s approach different from much of vaccine research is that it is “antigen-agnostic,” Serafini says. While many efforts in the field start out with a specific antigen that is already known to trigger an immune response, Atreca’s method may identify unknown or overlooked antigens that could be useful, he says.

Because of this, Atreca’s technology could be instrumental not only in combating infectious diseases, but also for developing products such as antibody-based cancer treatments or diagnostic tests for autoimmune disorders, Serafini says. But what drew the Gates Foundation’s eye was its potential for improving vaccine development. The Seattle foundation and the company are beginning their ongoing collaboration by focusing on malaria, HIV/AIDS, tuberculosis, and possibly other diseases in the first four years. The company anticipates that the foundation will contribute grant money for joint Atreca projects.

One possible tactic using the startup’s technology: Researchers could track the antibodies made by clinical trial participants after they receive a dose of an experimental vaccine. That could provide a scorecard on the effectiveness of the vaccine, through a tally of the antibodies known to be protective against the particular infection the vaccine is designed to prevent, Serafini says. An early look at the antibody population might provide quick clues to the outcomes of long trials.

Atreca will use the Gates Foundation’s $6 million investment to build its infrastructure and develop its technology, Serafini says. The startup, which now has about seven employees, is making some hires. It is also looking for other collaboration partners.

Serafini says potential partners may see advantages in a major feature of the “Immune Repertoire Capture’’ platform. It creates a route to manufacturing quantities of each antibody found in a patient scan, by identifying the DNA sequences that code for the each antibody.

The company envisions possible markets in four main business areas: therapeutic antibodies, vaccines, diagnostics, and reagents for research. Serafini says the technology platform may provide early commercial opportunities. But initial revenues from the sale of reagents, for example, would be used to finance R&D toward Atreca’s long-term ambitions—the development of new medical treatments.